Merge b32def6 into db8ad7a

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^(docs|.*test_files|cmd_line|dev_scripts)
+exclude: ^(docs|.*test_files|cmd_line)
 
 ci:
   autoupdate_schedule: monthly

dev_scripts/NIST Atomic Ionization Energies Output.html

@@ -84439,4 +84439,4 @@
 
 
 </body>
-</html>
+</html>

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -6,13 +6,6 @@
 identified with the separation plane algorithms (typically with coordination numbers >= 6)
 """
 
-__author__ = "David Waroquiers"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "2.0"
-__maintainer__ = "David Waroquiers"
-__email__ = "david.waroquiers@gmail.com"
-__date__ = "Feb 20, 2016"
-
 import itertools
 import json
 import os
@@ -33,6 +26,13 @@
 )
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
 
+__author__ = "David Waroquiers"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "2.0"
+__maintainer__ = "David Waroquiers"
+__email__ = "david.waroquiers@gmail.com"
+__date__ = "Feb 20, 2016"
+
 
 # Printing functions depending on the printing volume option
 def prt1(string, printing_volume):
@@ -47,7 +47,7 @@ def prt2(string, printing_volume):
 
 # Iterator function for the random permutations
 def random_permutations_iterator(initial_permutation, npermutations):
-    for ii in range(npermutations):
+    for _ in range(npermutations):
         shuffle(initial_permutation)
         yield initial_permutation
 
@@ -113,34 +113,34 @@ def random_permutations_iterator(initial_permutation, npermutations):
             raise ValueError("Wrong command line option for permutations_setup")
 
     # Class containing all the coordination geometries
-    allcg = AllCoordinationGeometries()
+    all_cg = AllCoordinationGeometries()
 
-    sepplane_cgs = []
+    sep_plane_cgs = []
     for coordination in range(1, 21):
-        symbol_name_mapping = allcg.get_symbol_name_mapping(coordination=coordination)
-        for symbol, name in symbol_name_mapping.items():
-            cg = allcg[symbol]
+        symbol_name_mapping = all_cg.get_symbol_name_mapping(coordination=coordination)
+        for symbol in symbol_name_mapping:
+            cg = all_cg[symbol]
             if cg.points is None:
                 continue
             if cg.algorithms[0].algorithm_type != "EXPLICIT_PERMUTATIONS":
-                sepplane_cgs.append(symbol)
+                sep_plane_cgs.append(symbol)
                 continue
     ncols = 5
-    nlines = int(np.ceil(float(len(sepplane_cgs)) / ncols))
-    sepplane_cgs_grid = []
-    for iline in range(nlines):
-        sepplane_cgs_grid.append([""] * ncols)
+    nlines = int(np.ceil(float(len(sep_plane_cgs)) / ncols))
+    sep_plane_cgs_grid = []
+    for _ in range(nlines):
+        sep_plane_cgs_grid.append([""] * ncols)
     for iline in range(nlines):
         for icol in range(ncols):
             ii = iline * ncols + icol
-            if ii >= len(sepplane_cgs):
+            if ii >= len(sep_plane_cgs):
                 break
-            sepplane_cgs_grid[iline][icol] = sepplane_cgs[ii]
+            sep_plane_cgs_grid[iline][icol] = sep_plane_cgs[ii]
 
     while True:
         # Printing all symbols
         print("Coordination geometries using a separation plane algorithm :")
-        print(tabulate.tabulate(sepplane_cgs_grid, tablefmt="grid"))
+        print(tabulate.tabulate(sep_plane_cgs_grid, tablefmt="grid"))
         print()
 
         # Define the coordination geometry
@@ -149,11 +149,11 @@ def random_permutations_iterator(initial_permutation, npermutations):
         )
         if cg_symbol == "q":
             break
-        if cg_symbol not in sepplane_cgs:
+        if cg_symbol not in sep_plane_cgs:
             print("Wrong geometry, try again ...")
             continue
 
-        cg = allcg[cg_symbol]
+        cg = all_cg[cg_symbol]
 
         print(f'Getting explicit permutations for geometry "{cg.name}" (symbol : "{cg_symbol}")\n')
 
@@ -220,7 +220,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
                 # Actual test of the permutations
                 csms, perms, algos, sep_perms = lgf._cg_csm_separation_plane(
                     coordination_geometry=cg,
-                    sepplane=algo,
+                    sep_plane=algo,
                     local_plane=local_plane,
                     plane_separations=[],
                     dist_tolerances=[0.05, 0.1, 0.2, 0.3, 0.5],
@@ -365,7 +365,7 @@ def random_permutations_iterator(initial_permutation, npermutations):
                     # Get the results for this algorithm and plane
                     csms, perms, algos, sep_perms = lgf._cg_csm_separation_plane(
                         coordination_geometry=cg,
-                        sepplane=algo,
+                        sep_plane=algo,
                         local_plane=local_plane,
                         plane_separations=[],
                         dist_tolerances=[0.05, 0.1, 0.2, 0.3, 0.5],

dev_scripts/chemenv/test_algos.py

@@ -58,7 +58,7 @@
         except Exception:
             raise ValueError(f"Could not turn {test} into integer ...")
         perms_iterator = []
-        for ii in range(nperms):
+        for _ in range(nperms):
             shuffle(myindices)
             perms_iterator.append(list(myindices))
 

dev_scripts/chemenv/test_algos_all_geoms.py

@@ -68,7 +68,7 @@
             except Exception:
                 raise ValueError(f"Could not turn {test} into integer ...")
             perms_iterator = []
-            for ii in range(nperms):
+            for _ in range(nperms):
                 shuffle(myindices)
                 perms_iterator.append(list(myindices))
 

dev_scripts/ionic_radii.csv

@@ -1 +1 @@
-Number,Name,Symbol,-3,-2,-1,1,2,3,4,5,6,7,83,Lithium,Li,,,,90,,,,,,,4,Beryllium,Be,,,,,59,,,,,,5,Boron,B,,,,,,41,,,,,6,Carbon,C,,,,,,,30,,,,7,Nitrogen,N,132 ,,,,,30,,27,,,8,Oxygen,O,,126,,,,,,,,,9,Fluorine,F,,,119,,,,,,,22,11,Sodium,Na,,,,116,,,,,,,12,Magnesium,Mg,,,,,86,,,,,,13,Aluminum,Al,,,,,,67.5,,,,,14,Silicon,Si,,,,,,,54,,,,15,Phosphorus,P,,,,,,58,,52,,,16,Sulfur,S,,170,,,,,51,,43,,17,Chlorine,Cl,,,167,,,,,26 ,,41,19,Potassium,K,,,,152,,,,,,,20,Calcium,Ca,,,,,114,,,,,,21,Scandium,Sc,,,,,,88.5,,,,,22,Titanium,Ti,,,,,100,81,74.5,,,,23,Vanadium,V,,,,,93,78,72,68,,,24,Chromium ls,Cr,,,,,87,75.5,69,63,58,,24,Chromium hs,Cr,,,,,94,,,,,,25,Manganese ls,Mn,,,,,81,72,67,47 ,39.5 ,60,25,Manganese hs,Mn,,,,,97,78.5,,,,,26,Iron ls,Fe,,,,,75,69,72.5,,39 ,,26,Iron hs,Fe,,,,,92,78.5,,,,,27,Cobalt ls,Co,,,,,79,68.5,,,,,27,Cobalt hs,Co,,,,,88.5,75,67,,,,28,Nickel ls,Ni,,,,,83,70,62 ls,,,,28,Nickel hs,Ni,,,,,,74,,,,,29,Copper,Cu,,,,91,87,68 ls,,,,,30,Zinc,Zn,,,,,88,,,,,,31,Gallium,Ga,,,,,,76,,,,,32,Germanium,Ge,,,,,87,,67,,,,33,Arsenic,As,,,,,,72,,60,,,34,Selenium,Se,,184,,,,,64,,56,,35,Bromine,Br,,,182,,,73 ,,45 ,,53,37,Rubidium,Rb,,,,166,,,,,,,38,Strontium,Sr,,,,,132,,,,,,39,Yttrium,Y,,,,,,104,,,,,40,Zirconium,Zr,,,,,,,86,,,,41,Niobium,Nb,,,,,,86,82,78,,,42,Molybdenum,Mo,,,,,,83,79,75,73,,43,Technetium,Tc,,,,,,,78.5,74,,70,44,Ruthenium,Ru,,,,,,82,76,70.5,,52 ,50 45,Rhodium,Rh,,,,,,80.5,74,69,,,46,Palladium,Pd,,,,73 ,100,90,75.5,,,,47,Silver,Ag,,,,129,108,89,,,,,48,Cadmium,Cd,,,,,109,,,,,,49,Indium,In,,,,,,94,,,,,50,Tin,Sn,,,,,,,83,,,,51,Antimony,Sb,,,,,,90,,76,,,52,Tellurium,Te,,207,,,,,111,,70,,53,Iodine,I,,,206,,,,,109,,67,54,Xenon,Xe,,,,,,,,,,,6255,Caesium,Cs,,,,181,,,,,,,56,Barium,Ba,,,,,149,,,,,,57,Lanthanum,La,,,,,,117.2,,,,,58,Cerium,Ce,,,,,,115,101,,,,59,Praseodymium,Pr,,,,,,113,99,,,,60,Neodymium,Nd,,,,,143 ,112.3,,,,,61,Promethium,Pm,,,,,,111,,,,,62,Samarium,Sm,,,,,136 ,109.8,,,,,63,Europium,Eu,,,,,131,108.7,,,,,64,Gadolinium,Gd,,,,,,107.5,,,,,65,Terbium,Tb,,,,,,106.3,90,,,,66,Dysprosium,Dy,,,,,121,105.2,,,,,67,Holmium,Ho,,,,,,104.1,,,,,68,Erbium,Er,,,,,,103,,,,,69,Thulium,Tm,,,,,117,102,,,,,70,Ytterbium,Yb,,,,,116,100.8,,,,,71,Lutetium,Lu,,,,,,100.1,,,,,72,Hafnium,Hf,,,,,,,85,,,,73,Tantalum,Ta,,,,,,86,82,78,,,74,Tungsten,W,,,,,,,80,76,74,,75,Rhenium,Re,,,,,,,77,72,69,67,76,Osmium,Os,,,,,,,77,71.5,68.5,66.5,53 77,Iridium,Ir,,,,,,82,76.5,71,,,78,Platinum,Pt,,,,,94,,76.5,71,,,79,Gold,Au,,,,151,,99,,71,,,80,Mercury,Hg,,,,133,116,,,,,,81,Thallium,Tl,,,,164,,102.5,,,,,82,Lead,Pb,,,,,133,,91.5,,,,83,Bismuth,Bi,,,,,,117,,90,,,84,Polonium,Po,,,,,,,108,,81,,85,Astatine,At,,,,,,,,,,76,87,Francium,Fr,,,,194,,,,,,,88,Radium,Ra,,,,,162 ,,,,,,89,Actinium,Ac,,,,,,126,,,,,90,Thorium,Th,,,,,,,108,,,,91,Protactinium,Pa,,,,,,116,104,92,,,92,Uranium,U,,,,,,116.5,103,90,87,,93,Neptunium,Np,,,,,124,115,101,89,86,85,94,Plutonium,Pu,,,,,,114,100,88,85,,95,Americium,Am,,,,,140 ,111.5,99,,,,96,Curium,Cm,,,,,,111,99,,,,97,Berkelium,Bk,,,,,,110,97,,,,98,Californium,Cf,,,,,,109,96.1,,,,
+Number,Name,Symbol,-3,-2,-1,1,2,3,4,5,6,7,83,Lithium,Li,,,,90,,,,,,,4,Beryllium,Be,,,,,59,,,,,,5,Boron,B,,,,,,41,,,,,6,Carbon,C,,,,,,,30,,,,7,Nitrogen,N,132 ,,,,,30,,27,,,8,Oxygen,O,,126,,,,,,,,,9,Fluorine,F,,,119,,,,,,,22,11,Sodium,Na,,,,116,,,,,,,12,Magnesium,Mg,,,,,86,,,,,,13,Aluminum,Al,,,,,,67.5,,,,,14,Silicon,Si,,,,,,,54,,,,15,Phosphorus,P,,,,,,58,,52,,,16,Sulfur,S,,170,,,,,51,,43,,17,Chlorine,Cl,,,167,,,,,26 ,,41,19,Potassium,K,,,,152,,,,,,,20,Calcium,Ca,,,,,114,,,,,,21,Scandium,Sc,,,,,,88.5,,,,,22,Titanium,Ti,,,,,100,81,74.5,,,,23,Vanadium,V,,,,,93,78,72,68,,,24,Chromium ls,Cr,,,,,87,75.5,69,63,58,,24,Chromium hs,Cr,,,,,94,,,,,,25,Manganese ls,Mn,,,,,81,72,67,47 ,39.5 ,60,25,Manganese hs,Mn,,,,,97,78.5,,,,,26,Iron ls,Fe,,,,,75,69,72.5,,39 ,,26,Iron hs,Fe,,,,,92,78.5,,,,,27,Cobalt ls,Co,,,,,79,68.5,,,,,27,Cobalt hs,Co,,,,,88.5,75,67,,,,28,Nickel ls,Ni,,,,,83,70,62 ls,,,,28,Nickel hs,Ni,,,,,,74,,,,,29,Copper,Cu,,,,91,87,68 ls,,,,,30,Zinc,Zn,,,,,88,,,,,,31,Gallium,Ga,,,,,,76,,,,,32,Germanium,Ge,,,,,87,,67,,,,33,Arsenic,As,,,,,,72,,60,,,34,Selenium,Se,,184,,,,,64,,56,,35,Bromine,Br,,,182,,,73 ,,45 ,,53,37,Rubidium,Rb,,,,166,,,,,,,38,Strontium,Sr,,,,,132,,,,,,39,Yttrium,Y,,,,,,104,,,,,40,Zirconium,Zr,,,,,,,86,,,,41,Niobium,Nb,,,,,,86,82,78,,,42,Molybdenum,Mo,,,,,,83,79,75,73,,43,Technetium,Tc,,,,,,,78.5,74,,70,44,Ruthenium,Ru,,,,,,82,76,70.5,,52 ,50 45,Rhodium,Rh,,,,,,80.5,74,69,,,46,Palladium,Pd,,,,73 ,100,90,75.5,,,,47,Silver,Ag,,,,129,108,89,,,,,48,Cadmium,Cd,,,,,109,,,,,,49,Indium,In,,,,,,94,,,,,50,Tin,Sn,,,,,,,83,,,,51,Antimony,Sb,,,,,,90,,76,,,52,Tellurium,Te,,207,,,,,111,,70,,53,Iodine,I,,,206,,,,,109,,67,54,Xenon,Xe,,,,,,,,,,,6255,Caesium,Cs,,,,181,,,,,,,56,Barium,Ba,,,,,149,,,,,,57,Lanthanum,La,,,,,,117.2,,,,,58,Cerium,Ce,,,,,,115,101,,,,59,Praseodymium,Pr,,,,,,113,99,,,,60,Neodymium,Nd,,,,,143 ,112.3,,,,,61,Promethium,Pm,,,,,,111,,,,,62,Samarium,Sm,,,,,136 ,109.8,,,,,63,Europium,Eu,,,,,131,108.7,,,,,64,Gadolinium,Gd,,,,,,107.5,,,,,65,Terbium,Tb,,,,,,106.3,90,,,,66,Dysprosium,Dy,,,,,121,105.2,,,,,67,Holmium,Ho,,,,,,104.1,,,,,68,Erbium,Er,,,,,,103,,,,,69,Thulium,Tm,,,,,117,102,,,,,70,Ytterbium,Yb,,,,,116,100.8,,,,,71,Lutetium,Lu,,,,,,100.1,,,,,72,Hafnium,Hf,,,,,,,85,,,,73,Tantalum,Ta,,,,,,86,82,78,,,74,Tungsten,W,,,,,,,80,76,74,,75,Rhenium,Re,,,,,,,77,72,69,67,76,Osmium,Os,,,,,,,77,71.5,68.5,66.5,53 77,Iridium,Ir,,,,,,82,76.5,71,,,78,Platinum,Pt,,,,,94,,76.5,71,,,79,Gold,Au,,,,151,,99,,71,,,80,Mercury,Hg,,,,133,116,,,,,,81,Thallium,Tl,,,,164,,102.5,,,,,82,Lead,Pb,,,,,133,,91.5,,,,83,Bismuth,Bi,,,,,,117,,90,,,84,Polonium,Po,,,,,,,108,,81,,85,Astatine,At,,,,,,,,,,76,87,Francium,Fr,,,,194,,,,,,,88,Radium,Ra,,,,,162 ,,,,,,89,Actinium,Ac,,,,,,126,,,,,90,Thorium,Th,,,,,,,108,,,,91,Protactinium,Pa,,,,,,116,104,92,,,92,Uranium,U,,,,,,116.5,103,90,87,,93,Neptunium,Np,,,,,124,115,101,89,86,85,94,Plutonium,Pu,,,,,,114,100,88,85,,95,Americium,Am,,,,,140 ,111.5,99,,,,96,Curium,Cm,,,,,,111,99,,,,97,Berkelium,Bk,,,,,,110,97,,,,98,Californium,Cf,,,,,,109,96.1,,,,